You mostly keep up with registrations for sales, so pick the one with the clout to make you more money over the lifetime of your goat project. Are your does and kids going to be registered via ABGA? Than keep up his paperwork with them...then tell others that he is also registered via the other one.

Who puts on the most shows in your area?

Who are the herds in your area or on the internet with similar quality stock to yours registered through? Vicki

I am not planning on raising boers at all. I have dairies and would like to have percentages to get a little better price for the kids. I was just wondering if it was like AKC vs. CKC (CKC is a crock in by book).

No, I disagree. Choose the more prevalent registry and use that one. But register him in your name so you can register his offspring as percentages. That way you can get more $$ for his kids than if you were to not register him/his kids.